8VVG | pdb_00008vvg

Kappa opioid receptor in complex with heterotrimerig Gi protein, bound to inverse agonist GB18


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Molecular mechanisms of inverse agonism via kappa-opioid receptor-G protein complexes.

Tyson, A.S.Khan, S.Motiwala, Z.Han, G.W.Zhang, Z.Ranjbar, M.Styrpejko, D.Ramos-Gonzalez, N.Woo, S.Villers, K.Landaker, D.Kenakin, T.Shenvi, R.Majumdar, S.Gati, C.

(2025) Nat Chem Biol 21: 1046-1057

  • DOI: https://doi.org/10.1038/s41589-024-01812-0
  • Primary Citation of Related Structures:  
    8VVE, 8VVF, 8VVG, 9D61

  • PubMed Abstract: 

    Opioid receptors, a subfamily of G protein-coupled receptors (GPCRs), are key therapeutic targets. In the canonical GPCR activation model, agonist binding is required for receptor-G protein complex formation, while antagonists prevent G protein coupling. However, many GPCRs exhibit basal activity, allowing G protein association without an agonist. The pharmacological impact of agonist-free receptor-G protein complexes is poorly understood. Here we present biochemical evidence that certain κ-opioid receptor (KOR) inverse agonists can act via KOR-G i protein complexes. To investigate this phenomenon, we determined cryo-EM structures of KOR-G i protein complexes with three inverse agonists: JDTic, norBNI and GB18, corresponding to structures of inverse agonist-bound GPCR-G protein complexes. Remarkably, the orthosteric binding pocket resembles the G protein-free 'inactive' receptor conformation, while the receptor remains coupled to the G protein. In summary, our work challenges the canonical model of receptor antagonism and offers crucial insights into GPCR pharmacology.


  • Organizational Affiliation
    • The Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa-type opioid receptor380Homo sapiensMutation(s): 0 
Gene Names: OPRK1OPRK
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens)
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Go to UniProtKB:  P41145
PHAROS:  P41145
GTEx:  ENSG00000082556 
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UniProt GroupP41145
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B [auth C]340Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth D]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1D [auth B]354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16251Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AD5 (Subject of Investigation/LOI)
Query on A1AD5

Download Ideal Coordinates CCD File 
F [auth A]methyl (2R,3R,3aS,5aR,9aS,9bS)-3-methyl-2-[(2S,6S)-6-methylpiperidin-2-yl]-1,2,3,3a,6,7,8,9,9a,9b-decahydro-3,5a-epoxycyclopenta[a]naphthalene-4-carboxylate
C22 H33 N O3
ONZIOCUDSJAMDE-BFUJQBEZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM144965
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesAT012075

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references
  • Version 2.0: 2025-08-13
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary